Organisms evolve through gene regulation: who/what is the regulator?

A tiny opossum's genome has shed light on how evolution creates new creatures from old, showing that change primarily comes by finding new ways of turning existing genes on and off.

"Evolution is tinkering much more with the controls than it is with the genes themselves," said Broad Institute director Eric Lander. "Almost all of the new innovation ... is in the regulatory controls. In fact, marsupial mammals and placental mammals have largely the same set of protein-coding genes. But by contrast, 20 percent of the regulatory instructions in the human genome were invented after we parted ways with the marsupial."

Protein coding genes are often regulated by non-coding DNA sequences. These sequences are not transcribed. An example of a regulatory sequence would be a promoter, a site where proteins that aid in the transcription of a coding gene can bind prior to the actual act of transcription. Another regulatory sequence might sit between the promoter and the coding gene, to which a repressor protein might bind. The repressor protein gets in the way of transcription proteins bound to the promoter, so the coding gene can't be transcribed. These are simple examples; there are many types of regulatory sequences throughout the genome of an organism.

Not at all. Random mutations can occur in the regulatory sequences too. I think the point here is that evolution of regulatory sequences can potentially have a greater effect than evolution of coding sequences, because many regulatory sequences work with multiple coding sequences. However, whichever type of sequence you have, the ultimate end product is eventually a protein (or lack thereof), upon which natural selection can act.

Not at all. Random mutations can occur in the regulatory sequences too.

The point is not that that could also happen and evolve organisms. The point is that that could also not happen, and still evolve organisms (through higher order gene regulation).

Take these statements for example:

Our report is not the first evidence of the existence of a specific mechanism directed toward genome rearrangements in stressed plants.

Our data suggests the existence of a specific, epigenetically controlled mechanism that promotes rearrangements in R-gene loci upon contact with a compatible pathogen.
http://nar.oxfordjournals.org/cgi/content/full/gkm029v1 [Broken]

Since epigenetics are "changes in gene function that occur without a change in the DNA sequence", the above link states, simply put, that there are mechanisms in those plants which are not controlled by gene mutations, yet do rearrange the genome. Basically, the plants detect environmental conditions that are unfavorable and then modify and reorganize specific parts of their genome in order to generate variations.

Changes in gene function due to epigenetics are still "genetic" in origin. Usually people refer to epigenetic regulation as any of the various chromosomal modifications that occur and can make transcription of certain genes more or less likely. The factors that affect these chromosomal modifications are themselves proteins coded for by DNA. So epigenetic regulators are just as subject to mutation as any other genes.

Also, rearrangement alone has the potential to powerfully effect transcription levels. Many regulators function via their position in relation to the genes they regulate. This is in addition to the fact that, as Cinncinnatus wonderfully put it, mutations can still be at the root of epigenetic regulator evolution.